Cost estimation for spinal muscular atrophy diagnosis using multiplex ligation-dependent probe amplification and droplet digital polymerase chain reaction

Objectives: Diagnosing spinal muscular atrophy necessitates determining the copy number of the SMN1 gene and the number of SMN2 gene copies, which correlate with disease severity. The present study aims to conduct a detailed cost-effectiveness analysis to determine SMN1 and SMN2 exon seven-copy numbers using droplet digital polymerase chain reaction (ddPCR) and multiplex ligation-dependent probe amplification (MLPA). Materials and Methods: Financial data were meticulously gathered from the institute’s operational test facility from January 2022 to December 2022. The annual costs for capital assets, operational expenses, consumables, and other supportive facilities were calculated. Probabilistic sensitivity analysis (PSA) was also conducted to evaluate statistical uncertainty. Results: The copy numbers of SMN1 and SMN2 gene exon seven were concordant between ddPCR and MLPA, with a significant correlation in test outcomes. The kappa coefficient was 1.000 and P = 0.0001. The annual capital and operational costs for ddPCR were INR 13,64,400 ($16,056) and INR 65,37,000 ($76,920), respectively. The MLPA’s annual capital and operational costs were INR 17,64,400 ($20,760) and INR 89,82,000 ($105,670). The calculated cost per test for ddPCR was INR 1,646 ($20), while for MLPA, it was INR 5,970 ($70). Furthermore, based on 10,000 simulations, the PSA determined that the ddPCR-based diagnosis is up to 83.6% cost-effective. It supports its integration into clinical practice for better patient outcomes and optimized healthcare costs. Conclusion: Utilizing ddPCR to determine the copy number of SMN1 and SMN2 gene exon seven offers cost-efficiency and time-saving advantages compared to alternative methods.